{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,8,23]],"date-time":"2023-08-23T20:12:24Z","timestamp":1692821544913},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Splice variation plays important roles in evolution and cancer. Different splice variants of a gene may be characteristic of particular cellular processes, subcellular locations or organs. Although several genomic projects have identified splice variants, there have been no large-scale computational studies of the relationship between number of splice variants and biological function. The Gene Ontology (GO) and tools for leveraging GO, such as GoMiner, now make such a study feasible.<\/jats:p>\n               <jats:p>Results: We partitioned genes into two groups: those with numbers of splice variants \u2264b and &amp;gt;b (b=1,\u2026, 10). Then we used GoMiner to determine whether any GO categories are enriched in genes with particular numbers of splice variants. Since there was no a priori \u2018appropriate\u2019 partition boundary, we studied those \u2018robust\u2019 categories whose enrichment did not depend on the selection of a particular partition boundary. Furthermore, because the distribution of splice variant number was a snapshot taken at a particular point in time, we confirmed that those observations were stable across successive builds of GenBank. A small number of categories were found for genes in the lower partitions. A larger number of categories were found for genes in the higher partitions. Those categories were largely associated with cell death and signal transduction. Apoptotic genes tended to have a large repertoire of splice variants, and genes with splice variants exhibited a distinctive \u2018apoptotic island\u2019 in clustered image maps (CIMs).<\/jats:p>\n               <jats:p>Availability: \u00a0Supplementary tables and figures are available at URL http:\/\/discover.nci.nih.gov\/OG\/supplementaryMaterials.html. The Safari browser appears to perform better than Firefox for these particular items.<\/jats:p>\n               <jats:p>Contact: \u00a0barry@discover.nci.nih.gov<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq335","type":"journal-article","created":{"date-parts":[[2010,7,11]],"date-time":"2010-07-11T20:55:14Z","timestamp":1278881714000},"page":"1945-1949","source":"Crossref","is-referenced-by-count":1,"title":["Ontogenomic study of the relationship between number of gene splice variants and GO categorization"],"prefix":"10.1093","volume":"26","author":[{"given":"Ari B.","family":"Kahn","sequence":"first","affiliation":[{"name":"1 Department of Bioinformatics, George Mason University, Fairfax, VA, 2Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 3SRA International, Inc., 4Tiger Team Consulting, Fairfax, VA, 5Department of Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH, 6Department of Statistics, Iowa State University, Ames, IA and 7Department of Bioinformatics and Computational Biology, M. D. Anderson Cancer Center, Houston, TX, USA"},{"name":"1 Department of Bioinformatics, George Mason University, Fairfax, VA, 2Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 3SRA International, Inc., 4Tiger Team Consulting, Fairfax, VA, 5Department of Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH, 6Department of Statistics, Iowa State University, Ames, IA and 7Department of Bioinformatics and Computational Biology, M. D. Anderson Cancer Center, Houston, TX, USA"},{"name":"1 Department of Bioinformatics, George Mason University, Fairfax, VA, 2Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 3SRA International, Inc., 4Tiger Team Consulting, Fairfax, VA, 5Department of Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH, 6Department of Statistics, Iowa State University, Ames, IA and 7Department of Bioinformatics and Computational Biology, M. D. Anderson Cancer Center, Houston, TX, USA"}]},{"given":"Barry R.","family":"Zeeberg","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, George Mason University, Fairfax, VA, 2Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 3SRA International, Inc., 4Tiger Team Consulting, Fairfax, VA, 5Department of Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH, 6Department of Statistics, Iowa State University, Ames, IA and 7Department of Bioinformatics and Computational Biology, M. D. Anderson Cancer Center, Houston, TX, USA"}]},{"given":"Michael C.","family":"Ryan","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, George Mason University, Fairfax, VA, 2Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 3SRA International, Inc., 4Tiger Team Consulting, Fairfax, VA, 5Department of Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH, 6Department of Statistics, Iowa State University, Ames, IA and 7Department of Bioinformatics and Computational Biology, M. D. Anderson Cancer Center, Houston, TX, USA"},{"name":"1 Department of Bioinformatics, George Mason University, Fairfax, VA, 2Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 3SRA International, Inc., 4Tiger Team Consulting, Fairfax, VA, 5Department of Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH, 6Department of Statistics, Iowa State University, Ames, IA and 7Department of Bioinformatics and Computational Biology, M. D. Anderson Cancer Center, Houston, TX, USA"},{"name":"1 Department of Bioinformatics, George Mason University, Fairfax, VA, 2Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 3SRA International, Inc., 4Tiger Team Consulting, Fairfax, VA, 5Department of Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH, 6Department of Statistics, Iowa State University, Ames, IA and 7Department of Bioinformatics and Computational Biology, M. D. Anderson Cancer Center, Houston, TX, USA"}]},{"given":"D. Curtis","family":"Jamison","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, George Mason University, Fairfax, VA, 2Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 3SRA International, Inc., 4Tiger Team Consulting, Fairfax, VA, 5Department of Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH, 6Department of Statistics, Iowa State University, Ames, IA and 7Department of Bioinformatics and Computational Biology, M. D. Anderson Cancer Center, Houston, TX, USA"},{"name":"1 Department of Bioinformatics, George Mason University, Fairfax, VA, 2Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 3SRA International, Inc., 4Tiger Team Consulting, Fairfax, VA, 5Department of Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH, 6Department of Statistics, Iowa State University, Ames, IA and 7Department of Bioinformatics and Computational Biology, M. D. Anderson Cancer Center, Houston, TX, USA"}]},{"given":"David M.","family":"Rockoff","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, George Mason University, Fairfax, VA, 2Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 3SRA International, Inc., 4Tiger Team Consulting, Fairfax, VA, 5Department of Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH, 6Department of Statistics, Iowa State University, Ames, IA and 7Department of Bioinformatics and Computational Biology, M. D. Anderson Cancer Center, Houston, TX, USA"}]},{"given":"Yves","family":"Pommier","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, George Mason University, Fairfax, VA, 2Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 3SRA International, Inc., 4Tiger Team Consulting, Fairfax, VA, 5Department of Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH, 6Department of Statistics, Iowa State University, Ames, IA and 7Department of Bioinformatics and Computational Biology, M. D. Anderson Cancer Center, Houston, TX, USA"}]},{"given":"John N.","family":"Weinstein","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, George Mason University, Fairfax, VA, 2Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 3SRA International, Inc., 4Tiger Team Consulting, Fairfax, VA, 5Department of Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH, 6Department of Statistics, Iowa State University, Ames, IA and 7Department of Bioinformatics and Computational Biology, M. D. Anderson Cancer Center, Houston, TX, USA"},{"name":"1 Department of Bioinformatics, George Mason University, Fairfax, VA, 2Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 3SRA International, Inc., 4Tiger Team Consulting, Fairfax, VA, 5Department of Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH, 6Department of Statistics, Iowa State University, Ames, IA and 7Department of Bioinformatics and Computational Biology, M. D. Anderson Cancer Center, Houston, TX, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,7,8]]},"reference":[{"key":"2023012508021927700_B1","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene Ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. 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Biochem."},{"key":"2023012508021927700_B7","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1007\/978-3-662-09728-1_7","article-title":"Alternative pre-mRNA splicing and neuronal function","volume":"31","author":"Black","year":"2003","journal-title":"Prog. Mol. Subcell. Biol."},{"key":"2023012508021927700_B8","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1016\/S0968-0004(00)01549-8","article-title":"Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases","volume":"25","author":"Blencowe","year":"2000","journal-title":"Trends Biochem. Sci."},{"key":"2023012508021927700_B9","doi-asserted-by":"crossref","first-page":"1031","DOI":"10.1002\/bies.10371","article-title":"Alternative splicing and evolution","volume":"25","author":"Boue","year":"2003","journal-title":"Bioessays"},{"key":"2023012508021927700_B10","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1146\/annurev.bi.56.070187.002343","article-title":"Alternative splicing: a ubiquitous mechanism for the generation of multiple protein isoforms from single genes","volume":"56","author":"Breitbart","year":"1987","journal-title":"Annu. Rev. Biochem."},{"key":"2023012508021927700_B11","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/S0896-6273(00)80751-5","article-title":"Alternatively spliced isoforms of nerve- and muscle-derived agrin: their roles at the neuromuscular junction","volume":"23","author":"Burgess","year":"1999","journal-title":"Neuron"},{"key":"2023012508021927700_B12","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1016\/S0168-9525(01)02626-9","article-title":"Alternative splicing: multiple control mechanisms and involvement in human disease","volume":"18","author":"Caceres","year":"2002","journal-title":"Trends Genet."},{"key":"2023012508021927700_B13","doi-asserted-by":"crossref","first-page":"1555","DOI":"10.1126\/science.1112014","article-title":"The transcriptional landscape of the mammalian genome","volume":"309","author":"Carninci","year":"2005","journal-title":"Science"},{"key":"2023012508021927700_B14","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1086\/514856","article-title":"The regulation of splice-site selection, and its role in human disease","volume":"61","author":"Cooper","year":"1997","journal-title":"Am. 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Biotechnol."},{"key":"2023012508021927700_B17","doi-asserted-by":"crossref","first-page":"D322","DOI":"10.1093\/nar\/gkj021","article-title":"The Gene Ontology (GO) project in 2006","volume":"34","author":"Gene Ontology Consortium","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012508021927700_B18","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1016\/S0301-0082(01)00007-7","article-title":"Alternative RNA splicing in the nervous system","volume":"65","author":"Grabowski","year":"2001","journal-title":"Prog. 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